PAT User Manual PDF
PAT User Manual PDF
PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 ) | 1
Citation
Ratcliff C, Gobbett D, Bramley R (2019) Precision Agriculture Tools (PAT) plugin v0.1.0 for QGIS: User
Manual. CSIRO, Australia.
Copyright
© Commonwealth Scientific and Industrial Research Organisation 2018. To the extent permitted by law, all
rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any
form or by any means except with the written permission of CSIRO.
Important disclaimer
The notes and software described here are based on a number of technical, circumstantial or otherwise
specified assumptions and parameters. The user must make their own assessment of the suitability for use
of the information or material contained in or generated from these notes. To the extent permitted by law,
CSIRO excludes all liability to any party for expenses, losses, damages and costs arising directly or indirectly
from using these notes and software tools.
Enquiries
Contact [email protected] for queries about the tools described in this manual.
2 | PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 )
Contents
PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 ) | 3
PAT - Precision Agriculture Tools
The Precision Agriculture Tools (PAT) plugin is a suite of open source tools developed by CSIRO for Precision
Agriculture (PA) data analysis. The tools run within Quantum Geographic Information System (QGIS) version
2.18 (QGIS Development Team 2017), a free and open-source desktop geographic information system that
supports viewing, editing, and analysis of geospatial data. PAT aims to provide an easy-to-use interface for
processing PA data through an established workflow developed for constructing maps using on-the-go data
(e.g. from yield monitors or EM38 soil surveys) as shown in Figure 1 and Table 1 (Bramley and Williams
2001; Taylor et al. 2007; Bramley et al. 2008; Bramley and Jensen 2014). It also includes tools for analysis of
remotely sensed imagery and some on farm experiments and for clustering map layers to create potential
management zones. Over time more tools and ‘how-to’ instructions will be added to expand the
functionality and usefulness for both practical and research purposes.
Create block
boundary
GPS block points Run kriging
using VESPER
Create
(Minasny
Raster
block grid VESPER et al. 2005)
Create polygon Block
from on-the-go boundary
data (cereal crops)
Clean, trim, & Create rasters
normalise data from VESPER
results
Legend
On-the-go
data PAT preferred tool
Process external to QGIS
How-to instructions
Datasets
Alternative method
Figure 1 The basic map production workflow used in PAT and some of the existing tools available for processing on-the-go
data.
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Table 1 Brief description of tools available in PAT
Import VESPER
Convert VESPER outputs to raster TIFF format.
Results
Generate a polygon block boundary from on-the-go data (e.g. from yield
Create Polygon
monitors) containing GPS points. The GPS points must cover the entire block
from On-The-Go
(not just be a set of points around the boundary - see page 50for instructions
GPS Point Trail Data
on creating a boundary from a set of surveyed data points)
Create rasters by
Rescale or rescaling (standardising) values between a fixed range (i.e. 0-1, or 0-
Normalise a Raster 255)
normalising values to a mean of 0 and standard deviation of 1
Generate Random Generate a selection of random pixels from a raster and save to a points
Pixel Selection Shapefile.
Extract Pixel Extract pixel statistics using a square neighbourhood footprint from multiple
Statistics for Points rasters at set locations.
Calculate Image Resample and smooth imagery to a larger pixel size, as well as calculate
Indices for Blocks indices such as PCD and NDVI.
Resample Image
Clip imagery to one or more blocks and resample to a different pixel size.
Band for Blocks
Create Zones with k-
Create zones with k-means clustering
means Cluster
User settings for PAT. Provides the ability to set data directories and the
Settings
location of VESPER (if installed).
PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 ) | 5
PAT Toolbar
PAT Menu
Figure 2 PAT toolbar, menu and log messages panel within QGIS
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1 Installing, Upgrading and Uninstalling
1.1 License
The PAT plugin for QGIS is free to download and use under a GPL V3 Open Source license. PAT license
details can also be found in the About tool under PAT menu. The companion Python library ‘pyprecag’ is
also freely available and is released under the CSIRO Open Source Software License Agreement (variation of
the BSD / MIT License). All source code and license files are available from https://github.com/CSIRO-
Precision-Agriculture.
1.2 Requirements
VESPER: To use the Run Kriging Using VESPER tool requires installation of VESPER (note: only available for
Microsoft Windows operating systems). VESPER is a kriging (map interpolation) program (Minasny et al.
2005). It needs to be installed independently if you would like to undertake kriging of maps using VESPER.
VESPER is not distributed with this plugin but is the recommended map interpolation tool. To download or
view more information on VESPER visit https://sydney.edu.au/agriculture/pal/software/vesper.shtml.
R 3.5.1+: The R statistical language (R Core Team 2018) is required to carry out the analytical processing for
the Whole-of-block Analysis (Section 2.13). R is not distributed with this plugin. If Whole-of-block analysis
is required then you must download and install R in addition to QGIS. The minimum R version suitable for
this is v3.5.1 Configuring QGIS to use R section on page 11.
QGIS LTR 2.18.21-26: Download and install the QGIS standalone long term release (versions 2.18.21 to
2.18.26). Note that the PAT tools do not currently work with QGIS version 3 or later.
QGIS 2.18.26 can be downloaded directly using these links.
32bit : http://download.osgeo.org/qgis/win64/QGIS-OSGeo4W-2.18.26-1-Setup-x86.exe
64bit: http://download.osgeo.org/qgis/win64/QGIS-OSGeo4W-2.18.26-1-Setup-x86_64.exe
Additional Python Packages: QGIS includes Python and numerous Python packages. However, PAT requires
the following additional packages: pyprecag, Fiona (Gilles et al 2011) and Rasterio (Gilles et al 2013). The
Fiona and Rasterio packages have been bundled with the PAT plugin and instructions on how to install
them are included.
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1.3 Installing PAT
Connect to the CSIRO Cloudstor Plugin Repository
1. In QGIS open the plugin manager (Plugins Menu → Manage and Install Plugins)
2. Select the Settings Section.
3. Tick Check for Updates and Show Experimental Plugins options.
4. Click Add
5. Enter the Name: CSIRO CloudStor Plugins.
6. Enter the following URL:
https://cloudstor.aarnet.edu.au/plus/s/vcIopbrD8KnMdbI/download
7. Leave authentication blank
8. Click OK.
You will receive an Failed Dependency Check message box and Error loading plugin messages. This is
expected, and is resolved by completing the next section titled Installing or Upgrading PAT Python
Dependencies.
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2. 3.
4.
While installing or upgrading PAT, a check will be completed to ensure the required Python packages are
installed on your system. If any of the images below appear, then this check has failed. This is normal.
PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 ) | 9
If the following message appears click No.
Click No
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Configuring QGIS to use R
If R is not installed and you launch the Whole-of-block analysis tools via the menu or toolbar you will a
warning message as shown.
When clicking OK you may get a Wrong value error message like this
PAT - Precision Agriculture Tools Plugin for QGIS ( January 2019 PAT v0.1.0 ) | 11
and your mouse cursor will remain a circle. To resolve treat the mouse circle as an arrow and
1. Under Providers, expand GRASS commands
2. Double click the text to the right of Msys folder, select and delete it and press the enter
key.
3. Click OK
4. Close and re-open QGIS to reset your mouse cursor.
It should now all work.
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1.4 Update PAT
If the Check for Updates option is checked on in the plugin manager, QGIS will advise the user if new
plugins are available, or if installed plugins have been updated. This notification is displayed in the QGIS
interface’s status bar as shown below. It is recommended that Check for Updates is checked.
To Update
1. In QGIS open the Plugin Manager by clicking on the link in the status bar or via Plugins.
Menu → Manage and Install Plugins
2. Either select the Upgradeable left side tab or search for your plugin.
3. Upgrade by selecting the PAT plugin and click Upgrade plugin
A check will be run to ensure the Python packages required by PAT are installed and are of the correct
version. If this check fails follow the instructions in Installing or Upgrading PAT Python Dependencies to
upgrade the dependencies.
2.
.
3.
.
1.
.
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1.5 Uninstall PAT
If you wish to uninstall PAT and its Python dependencies you must first uninstall the Python dependencies,
followed by the plugin as instructed below.
1. Navigate to the current user’s PAT installation directory. This folder is listed in as Plugin Dir in the
settings dialog as shown highlighted in yellow below.
PAT Python dependencies should be uninstalled PRIOR to uninstalling the PAT plugin. The plugin can be
uninstalled in one of two ways.
1. Via the QGIS Plugin Manager
a. In QGIS, open the plugin manager, and find the PAT plugin.
b. Click Uninstall plugin.
2. Via Windows Explorer.
a. Navigate to the current users PAT installation directory as show in 1.5.1.1 above.
b. Delete the entire pat folder.
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2 Individual Tools
2.1 Create Block Grid
Summary
This tool converts polygon features such as a block boundary to a raster grid using a set pixel size. This is a
critical part of setting up the analysis environment for creating maps from on-the-go data because it
generates the base grid onto which maps will be interpolated, by using the outer most extent of the block
boundary as the ‘frame’ for the grid. Page 50 details how to generate a block boundary if one is not already
available.
The raster outputs created by the Block Grid tool are:
a TIFF raster and
a grid file of X,Y point values used by VESPER for kriging.
Areas inside the polygon boundary will be assigned a value of 1 while areas outside will be assigned a no-
data value of -9999.
Dialog
Select a polygon A layer containing the block boundary polygon features in a projected coordinate
layer system to be converted to the raster outputs.
If checked, will only use the selected features, if unchecked, all the features will be
Use selected Default is
used. Useful in creating a grid for a single field from a boundary layer comprising
features unchecked
more than one field.
The pixel size to assign to the raster outputs. This is expressed in metres.
Recommended Values:
0.00m to 6 km Viticulture: 2 m
Pixel size (m)
Default is 2 m Sugarcane: 2 m
Broadacre grains: < 200 ha 5 m
> 200 ha 10 m
Snap extent to Default is Snap the output raster extent to a factor of the pixel size. This will ensure adjacent
factor of pixel Size checked rasters use a common origin which is important for future analysis.
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2.2 Clean, Trim, Normalise Point Data
Summary
This tool processes on-the-go data files (e.g. from a yield monitor or EM38 soil survey) containing GPS
coordinates recorded as latitude and longitude in decimal degrees, to output point values in a projected
coordinate system. The tool also applies cleaning and filtering rules.
This tool:
retains all columns (except coordinate columns) from the original file.
converts coordinate columns to a projected coordinate system and renames them to Easting and
Northing. An additional column (EN_EPSG) will be created and assigned the EPSG number for the
projected coordinate system used to reproject data. An EPSG number is an international numbering
system for coordinate systems (see http://www.epsg.org/)
optionally saves a Shapefile version matching the output CSV file. A second Shapefile will also be
saved containing the string _removed in its filename. This Shapefile will contain all the points the
filter discards and will be attributed by filter type. The description of the values can be found in
Table 2
As part of the filtering process, the tool may rename some data columns to adhere to Shapefile column
name limitations. The new names are displayed as a PAT log message and written to the log file. For more
information on the location of the saved log file and temporary folder refer to the Technical Notes section
on page 49.
Once processing is complete, the results of filtering are shown as a PAT log message. Only filters which
remove points are listed. When iteratively filtering, results of all iterations are shown. An explanation of
these is shown in Table 2.
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Dialog
Choose whether to use GPS data currently loaded in QGIS as a Points Layer
Options
Filename include XLS, The filename of the table file.
TXT, CSV
Default is the The QGIS layer name for the output point
Layer name
sheet name. and/or polygon files.
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If checked, use the selected features to
Default is clip the input points.
Use selected features
unchecked
If unchecked, all the features will be used.
Derived from The name and path of the output CSV file
Save CSV file
layer name containing the final data points.
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Notes
Table 2 A description of the filter type used when reporting filtering results.
Points removed during the standard deviation (std) iteration (iter) number 1 and uses 3 standard
03 3.0 std iter 1
deviations.
Points removed during the standard deviation (std) iteration (iter) number 2 and uses 3 standard
04 3.0 std iter 2
deviations.
Points removed during the standard deviation (std) iteration (iter) number 3 and uses 3 standard
05 3.0 std iter 3
deviations.
06 pointXY (1.0 m) Points removed which are spaced at less than the specified distance apart, in this case 1m
Points removed after sorting by the X coordinate, which are spaced at less than the specified
07 pointX (1.0 m)
distance apart, in this case 1 m
Points removed after sorting by the Y coordinate, which are spaced at less than the specified
08 pointY (1.0 m)
distance apart, in this case 1 m
Pts remaining The number of points left after filtering occurs.
The following notification occurs when a delimited text file contains invalid characters in a column
name. A copy of the file with corrected column names will be made in the PAT temporary folder
(location shown in PAT log message). For more information on the location of the saved log file and
temporary folder see the Technical Notes section on page 49.
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2.3 Run Kriging Using VESPER
Summary
This tool is used for mapping on-the-go data, such as are collected by a yield monitor or an EM38 soil
survey, following established protocols (Bramley and Williams 2001; Taylor et al. 2007; Bramley et al. 2008;
Bramley and Jensen 2014) using local block kriging. It will create a VESPER control file and collate the files
required for kriging. The following files will be created in a VESPER sub-folder located in the specified
output folder.
the VESPER control file. The control filename will be used as a base to derive other VESPER output
files like the kriged map result.
a subset of data to krige. All non-required columns are deleted.
a Windows batch file (Do_VESPER.bat) which can be used to launch VESPER processing for all
control files in the VESPER sub-folder. This process can be run outside of QGIS and the
Python/pyPrecAg environment.
Any files matching the control file name will be deleted from the VESPER sub-folder including VESPER
kriged results, to ensure that the files remaining belong to the newly create control file. If you want to
retain old versions, use a different name for the control file.
The coordinate system of the CSV file will be determined by interrogating the EN_EPSG or ENEPSG columns
generated as a by-product of running the Clean, Trim, Normalise Point tool. If the resulting value cannot be
found or is incorrect, the coordinate system can be set manually. The resulting EPSG number will be stored
within the control file and later used when converting VESPER outputs into raster TIFF format.
To krige (run) VESPER control files from within QGIS, VESPER must already be installed on the PC and
configured in the PAT settings (see Settings Tool on page 48).
If the Run VESPER Kriging Now option is checked the output control file will be launched in VESPER and
kriged immediately. Running this tool multiple times will add each output control file to the VESPER queue
and run consecutively. The QGIS status bar is used to manage the queue; currently the queue can only be
displayed and cleared. On the completion of each VESPER run, if the Convert VESPER Files to Raster and
Load in QGIS option is checked the kriged results will be import to TIFF files and loaded into QGIS.
If the Run VESPER Kriging Now option is unchecked the tool will create the VESPER control, data and batch
files in the selected folder allowing the user to run VESPER in their own time.
When Run VESPER Kriging Now or Convert VESPER Files to Raster and Load in QGIS options are unchecked
the Import VESPER Results (post VESPER) tool can be used to import VESPER kriged results to TIFFs then
loaded into QGIS.
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Dialog
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If checked, the name will be generated from the first 20
characters of the input CSV file, the string ‘control’ and the
Auto create Krige column.
control file name
Uncheck this option to prevent manual edits from being
overwritten when changing source CSV file or Krige column.
Configure to show
Checking this option will display the map
VESPER graph and Default is
and graph while VESPER is running but
map graphics unchecked
will increase the processing time.
while kriging
Run VESPER Default is Add the control file to the VESPER Queue
kriging now checked for processing.
EXTEN
DESCRIPTION FILENAME EXAMPLE
SION
Files required by VESPER and copied to the VESPER output folder
VESPER control file <first 20 characters CSV file>_< first 10 characters of krige column>_control .txt swblock_YldMassDry_control.txt
VESPER grid file <control file name> where control is replaced by vespergrid .txt swblock_YldMassDry_vespergrid.txt
VESPER data file <control file name> where control is replaced by vesperdata .csv swblock_YldMassDry_vesperdata.csv
If converting VESPER files to raster is checked or the Create Rasters from VESPER Results tool is used
Kriged Prediction TIFF <control file name> where kriged is replaced by PRED .tif swblock_YldMassDry_PRED.tif
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source: VESPER Krige result above
Standard Error TIFF
<control file name> where kriged is replaced by SE .tif swblock_YldMassDry_SE.tif
source: VESPER Krige result above
Confidence Interval (CI) metadata text file <control file name> where control is replaced by CI .txt swblock_YldMassDry_CI.txt
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2.4 Import VESPER Results
Summary
This tool converts the output files generated by VESPER into raster TIFFs.
The output filenames will be created using the VESPER control file name as a base and demonstrated in the
Prepare Data for Kriging using VESPER Tool - File Naming Conventions section on page 22.
The files created include:
a TIFF file representing the predicted (kriged) value; these are the values used to generate the
resulting map.
a TIFF file representing the standard error (SE) of the kriging prediction.
a text file containing the calculated median kriging prediction SE and the 95% confidence interval
for the map. This is important information for testing the significance of the difference between
different zones when different map layers are clustered to generate potential management zones.
The coordinate system to be assigned to the rasters will be extracted from the value stored within the
control file. If the coordinate system cannot be found or is incorrect, it can be selected manually.
Dialog
VESPER Control File: A VESPER control file used to identify VESPER results files and convert to rasters.
Coordinate System By default it is This is the coordinate system of the VESPER results.
for CSV File: extracted from the
input control file.
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2.5 Create Polygon from On-The-Go GPS Point Trail Data
Summary
Having a block boundary polygon is central to many of the PAT processing steps. Boundary polygons are
used to constrain data to a fixed extent. It is preferably that a boundary polygon is created by collecting
accurate GPS points around the block and editing them in QGIS to create polygons (refer to How-To -
Create a block boundary polygon from a CSV of GPS collected points on page 50 for instructions on this
method). However, if accurate GPS data for the boundary is not available, then a less accurate block
boundary polygon can be created using this tool, based upon a file of on-the-go GPS points (i.e. from a yield
monitor or EM38 survey data). Note that this method is not preferred, but the tool is provided as a ‘quick
fix’ for those wishing to generate maps in the absence of surveyed block or field boundaries.
As the process involves a dot-to-dot approach, it is critical that the input file of points are in order (i.e.
sorted by an increasing time sequence - as would be normal for data collected by an on-the-go sensor such
as yield monitor). For efficiency, points can be thinned by removing points closer than a set distance apart
as justified by the accuracy of the GPS. Resulting points will be connected to form lines and then converted
to polygons.
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Dialog
Choose whether to use GPS data currently loaded as a QGIS Points Layer
Options include
Filename The filename of the table file.
XLS, TXT, CSV
By default will
X column attempt to match
The columns representing the X and Y
to X,Y, longitude,
Y column coordinates within the input file.
latitude; lon, lat
etc.
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0.00 to 100.00
Thin distance Any points spaced at less than the
Default is 1
(m) minimum distance apart will be removed.
Use 0 to omit
Projected
The output projected coordinate system
coordinate
of the Shapefile.
system
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Notes
The following notification occurs when a delimited text file contains invalid characters in the
column name. A copy of the file will be made in the PAT temporary folder containing corrected
column names as specified in the PAT log message and to file. For more information on the location
of the saved log file and temporary folder see the Technical Notes section.
A warning is triggered when the resulting polygon is considered stripy or noisy. This can usually be
corrected by increasing the buffer and shrink distances.
The following error is caused when the wrong coordinate system is applied to the input source file
or layer. Thinning and/or clipping will result all points being removed leaving no points for further
processing
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2.6 Rescale or Normalise a Raster
Summary
This tool rescales or normalises a raster and outputs to a new TIFF file. Existing no-data values will be
ignored in any calculation.
Rescale will adjust the raster between the specified values (e.g. output values all in the range 0 to
1)
Normalise will adjust the raster to a mean of zero and standard deviation of one
Such re-scaling is useful when you wish to compare several map layers, for example, yield maps for several
years.
Dialog
Options:
Rescale – adjust values to a fixed range
Method Default is rescale
Normalise – adjust values to a mean of zero and a standard deviation of
one
Rescale between
Default 0 to 255 The range of values used with rescaling.
(when selected)
Default will be
Save as Shapefile derived from the The output Shapefile to be created.
input layer name
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2.7 Generate Random Pixel Selection
Summary
This tool is used to select randomly distributed pixel locations from an existing raster and save them to a
point Shapefile. Pixels will be selected from areas inside the raster extent which contain valid data. The
resulting points will be located in the centre of the chosen pixel and the output shapefile will contain
columns representing the X and Y coordinates. This tool provides the key location input for the Extract Pixel
Statistics for Points tool described on the following page.
Dialog
Generate random
Default is band 1 The number of pixels to randomly select
sample pixels
The raster to use as the base for selecting pixels. No-data pixels will be exempt
Select a raster layer
from selection.
Default will be
Save as Shapefile derived from the The output Shapefile to be created.
input layer name
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2.8 Extract Pixel Statistics for Points
Summary
Extract pixel statistics for points is used to extract pixel statistics from multiple rasters using a pre-defined
set of points. These points could be identified using the Generate Random Pixel Selection tool described on
the previous page. Statistics are calculated on pixel values within a square neighbourhood and extracted to
a CSV file. This tool is useful when relationships are being sought between different maps layers – for
example, a regression or correlation analysis between yield and soil map data.
Applying a neighbourhood filter to rasters is useful for removing (smoothing) small anomalies introduced
from instrument inaccuracies or on-the-go movement. The neighbourhood consists of a centre pixel and a
number of pixels forming a square around the central pixel, as shown in Figure 3.
9 x 9 For example, a mean statistic for a 3x3 neighbourhood on 2 m pixels, will
7 x 7 calculate the mean of the central pixel (red) and the surrounding 3x3
5 x 5
3 x 3
area of 8 pixels (yellow) equating to 36 m2 on ground.
C Pixels designated no-data will be excluded from the statistical
calculation. However, a central no-data pixel may be assigned a value if
at least one pixel in the neighbourhood has a valid value.
Figure 3. A representation of the Currently, the statistical methods supported by this tool are: mean,
3x3, 5x5, 7x7, 9x9 neighbourhood standard deviation, co-efficient of variation (CV), minimum, maximum
size around a central pixel (C) as is and a count of pixels contributing to the statistical calculation.
used when calculating filtered
The output values are saved to a CSV data file. Column names for each
statistics.
raster and statistic combination are explained below.
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Dialog
Derived from The name and path of the output CSV file
Save CSV file
layer name containing the final data points.
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File and Column Naming Conventions
<> denotes an existing element or input
non-alphanumeric characters are removed with the exception of hyphens (-) and underscores ( _ ).
Output Filenames:
CSV filename <QGIS points layer name>_pixelvals.csv
Column Names:
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2.9 Calculate Image Indices for Blocks
Summary
Many providers of remotely sensed imagery deliver data to clients as multi band files. The Calculate Image
Indices for Blocks tool is used to calculate indices for a multi band image and aligns the output to the extent
and pixel size of a block grid. Indices currently supported are Normalised Difference Vegetation Index
(NDVI); the ‘simple ratio’ or Plant Cell Density index (PCD); Green Normalised Difference Vegetation Index
(GNDVI); Chlorophyll Red-Edge index (CHLRE); and Normalised Difference Red-Edge index (NDRE).
Table 3 describes how these indices are calculated.
Each band in the image file is mapped to a spectral band e.g. Red, Red-edge, Near Infrared and is then used
to calculate relevant image indices. In the case of vineyard data, if a non-vine mask is present in an existing
band of the image, it can be used to remove non-vine signals prior to the resampling and alignment to the
block grid. This will ensure that spectral signatures relating to ground cover are excluded from the resulting
image outputs. This non-vine masking is not relevant for broadacre crops.
An optional block boundary polygon layer, and a column containing the block name or ID, can be used to
separate the resulting images into individual blocks. By default, if no column is specified, then all polygons
are assumed to be from the one block and will be processed accordingly. If no block boundary layer is
specified, then a single polygon outlining the image (excluding no-data) will be used. The output from this
tool will be aligned to a block grid that will be identical to the one created separately using the Create Block
Grid on page 15.
𝑁𝐼𝑅
Plant Cell Density Index (PCD) PCD =
𝑅𝑒𝑑
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Dialog
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The projected coordinate system to apply to the output files.
By default it will calculate the relevant coordinate system
Projected from the input image or block boundary’s coordinate system.
coordinate
system
Note: If in Australia then MGA GDA 1994 zones, will be used
– see Figure 5 on page 49.
Filenames:
Output Folder:
A new folder based on the image name is created in the output folder and
all created images are saved here.
<output_folder>\<image_name> C:\data\vineyard\rgbi_jan_50cm_84sutm54_tif
In this example the image rgbi_jan_50cm_84sutm54.tif is used to create a
new folder called rgbi_jan_50cm_84sutm54_tif.
Image Names:
The TIFF file resampled to 2m pixels for the Normalised Difference
<block_id>_<index>_<pixel_size>.tif B1_NDVI_2m.tif
Vegetation Index (NDVI) created for block id/name of B1.
The TIFF file resampled 250cm pixels for the Plant Cell Density (PCD) Index
PCD_250cm.tif
created without specifying a block id column.
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2.10 Resample Image Band for Blocks
Summary
Resample Image Band for Blocks is used to resample, align and smooth an existing band of an image to
match a block grid.
An optional block boundary polygon layer and a column containing the block name or ID, can be used to
separate the resulting images into individual blocks. By default, if no column is specified, then all polygons
are assumed to be from the one block and will be processed accordingly. If no block boundary layer is
specified, then a single polygon outlining the input image will be used.
The output from this tool will be aligned to a block grid that will be identical to the one created separately
using the Create Block Grid on page 15.
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Dialog
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File Naming Conventions
<> denotes an existing element or input
non-alphanumeric characters are removed from strings with the exception of hyphens (-) and underscores ( _ ).
Filenames:
Output Folder:
A new folder based on the image name is created in the output folder and
all created images are saved here.
<output_folder>\<image_name> C:\data\vineyard\area1_rgbi_jan_50cm_84sutm54_tif
In this example the image area1_rgbi_jan_50cm_84sutm54.tif is used to
create a new folder called area1_rgbi_jan_50cm_84sutm54_tif.
Image Names:
<block_id>_<Band>_<pixel_size>.tif B1_Band6_2m.tif The TIFF file where Band 6 is resampled to 2m for block id/name of B1.
The TIFF file where Band 7 is resampled 250cm pixels without specifying a
Band7_250cm.tif
block id column.
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2.11 Create Zones with k-means Clusters
Summary
This tool allows zones to be created by performing k-means clustering on multiple rasters (i.e. map layers)
to create clusters of similarity by minimising variability within clusters while maximising variability between
clusters. If significant differences between clusters are observed then the clustered results can be used as
potential management zones.
Raster files with the same single pixel size, and coordinate systems are used as inputs and the common
area of overlap will be used to generate an output TIFF containing the clustered result.
On completion of k-means clustering, the mean and standard deviation for each zone/cluster and source
raster combination will be calculated and written to a CSV File alongside the output TIFF file as well as
being displayed in PAT’s log messages panel.
Dialog
The name and path of the output TIFF file representing the zones.
Save TIFF file In addition, a statistics CSV file will be written to disk along with the TIFF, and results printed to PAT’s log
messages panel.
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File and Column Naming Conventions
<> denotes an existing element or input
non-alphanumeric characters are removed from strings with the exception of hyphens (-) and underscores ( _ ).
FILENAMES:
Output TIFF
Naming Rule: k-means_<n_clusters>clusters_<n_rasters>rasters_<pixel_size>.tif
Example: k-means_3clusters_5rasters_2m.tif
Description: A 2m pixel TIFF file for 3 k-means clusters using 5 input rasters
Output Statistics CSV < output TIFF name> where .tif is replaced by _statistics.csv
Notes
To successfully use this tool, all input raster files must contain the coordinate system internal to the
file. When a file without a coordinate system is loaded into QGIS, an external coordinate system
will be applied based on your QGIS settings. These files cannot be used by this tool. The user will be
notified of this when launching the tool as follows.
Clicking on view will open the PAT Log Messages Panel and provide a list of those images. Users can
then use the Assign Projection Tool from the Raster -> Projection menu to assign an internal
coordinate system to the files. If the Assign Projection tool is unavailaalbe activate the GDALTools
plugin .
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2.12 Create Strip Trial Points
Summary
This tool is used to generate the data needed to implement the moving window t-test method of Lawes
and Bramley (2012) for analysis of simple strip trials. It may be useful to users who, for example, have
implemented an N-rich strip in their cereal paddock, or who want to compare a row of vines that have been
pruned differently to the rest of a vineyard. The tool uses a line representing the centre of a strip trial and
creates points along and at an offset to the line; the offset points are those for comparison with the strip
points. In this current version of PAT, use of this tool needs to be followed by using the strip and offset
points generated as input to the Extract Pixel Statistics for Points tool to extract values from map raster(s)
relevant to the strip experiment (e.g. a yield map) which can then be analysed outside of PAT. In a future
version, the entire analysis will be provided in PAT but in the meantime follow the instructions in
Analysing strip trial data using the moving window t-test on page 54.
Points are placed along the line using the nominated distance between points. In addition, two sets of
points are placed at the offset distance either side of the line. This allows the strip data, to be compared to
data from the neighbouring (control) area.
Each point is assigned a Side, PointID and line_dist values which are saved in the shapefile. The side
attribute represents one of the following:
C – centre line;
R – Right offset to centre line
L – Left offset to centre Line.
Left and right values are assigned based on the original drawing direction of the line not how they appear
on screen. The same PointID assigned to the centre line is also applied to the relevant L/R point.
The line_dist represents the distance in metres of the point from the start of respective line. The distances
for the L/R sides are calculated from the start of the offset line, not the centre line.
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Dialog
Strip trial lines: The layer containing the strip trial lines.
Distance between 1 – 500.00 The distance used to space points along the line. In this instance, users are advised
points (m): Default is 20.0 to select a value appropriate to their trial rather than accepting the default.
1 – 500.00
Offset distance (m) The distance used to offset the points from the line.
Default is 30.0
Derived from
Points shapefile: The name and path of the output points shapefile.
layer name
Default is
unchecked.
Save line shapefile: The name and path of the output points shapefile.
Derived from
layer name.
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2.13 Whole-of-block Analysis
Summary
Figure 4 An example of a whole-of-block experiment conducted in a 4.8 ha Clare Valley vineyard. Panten and
Bramley (2011) provide further information
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The purpose of the Whole-of-Block analysis tool is to predict treatment responses and their differences
over the entire experimentation area as illustrated by Figure 4. Similar to the use of VESPER for kriging, this
tool interpolates point data (low or high density) to the area of the entire block. Low density data would
typically include up to a few hundred points, perhaps collected through hand sampling, dispersed across a
block, whereas high density data includes a few thousand or more points, typically collected using a sensor
such as a yield monitor. The tool will handle either two or three treatments, and will identify areas of the
block where the treatments are significantly different from each other. To address the technical and
computational challenges in this analysis, the tool uses fast and efficient global and local cokriging
techniques.
Use of R
This tool is somewhat different from the other PAT tools in that it uses the R statistical language
(http://r-project.org/) to carry out the analytical processing. This means that R must be installed on
your PC for this to work – see Configuring QGIS to use R on page a11. The minimum R version suitable
for this is v3.5.1.
Algorithm for the Local Cokriging System – a brief commentary on the data radius used
A spatially-varying local co-kriging method is used to balance the trade-off between the computation
efficiency and prediction accuracy. We use a neighbourhood radius r(s) to identify neighbours for location
s.
For subregions with lower density observations, such as at the corners, or edges of a farm field, the
neighbourhood radius required by local cokriging will be relatively bigger to ensure the stability of the
estimated cross-variograms and balance the number of observations from different treatments within the
neighbourhood.
For high density datasets we will use a relatively small neighbourhood radius, and ensure it will change
relatively smoothly across the field. This adaption is achieved by two specific algorithm choices. Firstly, an
initial neighbourhood radius is selected automatically based on the observation density and achieving a
reasonable balance in the number of observations from different treatments. This neighbourhood radius
increases iteratively to include more observations if the current radius is not large enough to meet
prediction quality criteria. Secondly, a spatial-varying neighbourhood radius surface is estimated based on
neighbourhood radius values from a subset of locations. This exploits the spatial-smoothness of the
neighbourhood radius and provides a better default neighbourhood radius from which to optimise .
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Dialog
Input points
layer A text format data file (CSV format) containing the experimental data that has been loaded into QGIS. The file
should be a minimum of four columns containing, the following:
Easting and The names of columns in the CSV data file containing the projected Easting and Northing point coordinates
Northing
The name of column in the CSV data file containing the treatment applied at each point.
Treatment
The treatments can be represented by numbers (1,2,3), short characters (“AM”,”BL”,”CS”) or text 10
column
characters or less without spaces like (“Control“,“Mulch”,”Cover_crop”).
The name of column in the CSV data file containing the measured treatment response (e.g. Yield) at each
Data column point.
Input Block The grid onto which treatment predictions, differences and standard errors are to be interpolated by the
Grid or tool.
Prediction The block grid created by PAT Create Block Grid tool is ideal for this, or it can be a raster (TIF) file with the
Grid same coordinate system as the Input Points Layer.
Covariance Default is
Exponential (default); users may also select Spherical and Gaussian models
Model Exponential
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Default is Only applicable to the Local Cokriging method, and allows a user to define an initial
unchecked neighbourhood radius. If this option is ticked then user should define the "Input
User Defined
Neighbourhoo Neighbourhood Size in Metres". The default is 30 m. A suggested starting value can be
d radius for Default is calculated as 15 times the pixel size of the block grid. However, if "User Defined
Local 30m or 15 Neighbourhood for Local Cokriging" is not ticked then the initial neighbourhood radius will be
Cokriging times the chosen as a function of total number of data points and corresponding number of treatments.
pixel size This is the recommended starting point for using this tool.
Filenames:
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2.14 Settings
Summary
Dialog
Set the location of the VESPER executable. If this is not found or specified, VESPER
Location of VESPER Exe
cannot be run, but relevant VESPER input files can still be created.
When checked, various intermediate files will be written to disk to assist with
Debug (Keep Outputs)
error/debugging analysis. However, this will slow down processing.
If checked, any files written to disk, or created in memory will be loaded into QGIS
Display Memory/Temporary Layers
into a grouped layer labelled DEBUG and can be used for error/debugging analysis.
* By default this will be the PAT sub-folder in the user’s home directory. To quickly navigate here type %homepath%/PAT in the
address bar of Windows Explorer.
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3 Technical Notes
PAT makes use of the CSIRO-developed pyPrecAg Python module which is an open source Python
package containing a range of specialised analysis functions.
All intermediate files created while processing are located in the PrecisionAg folder of the user’s
temporary folder. To quickly navigate to the temporary folder, type %temp%/PrecisionAg in the
address bar of windows explorer. This folder is deleted when QGIS exits.
All progress, messages and errors are displayed in the PAT tab of the Log Panel as shown in Figure 2
and are saved to a log file located in the PrecisionAg folder of the user’s temporary folder. A list of
important paths including the location of temp and the user’s plugin folder.
A Users QGIS Plugin folder can be found by typing %homepath%/.qgis2/python/plugins into the
address bar of Windows Explorer.
When a projected coordinate system is predicted from the source data, and the data is identified as
being in Australia, the Map Grid of Australia (MGA) reference system is used.
The MGA zones align closely with the SUTM zones, but use the 1994 Geocentric Datum of Australia.
Figure 5 shows the position of these the MGA zones.
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4 How-To’s
4.1 Create a block boundary polygon from a CSV of GPS collected points
1. Using the New Shapefile Layer tool from the
manage layers toolbar (or Layer menu -> Create
Layer -> New Shapefile Layer) create a new
polygon shapefile adding the relevant
coordinate system* and attribute fields you
require. Clicking OK will prompt you for the
location to save the shapefile.
More information on coordinate systems can
be found at
2. Set a style and labelling to the polygon
layer. A hatching polygon fill works well for
editing.
3. Launch the Add Delimited Text
Layer tool from the manage layers
toolbar (or Layer menu-> Add Layer -> Add
Delimited Text Layer) and load your GPS CSV
file as a layer into QGIS.
Hint: Your coordinate system is probably
WGS 84.
4. If required, load other vector or raster data,
like imagery, which can be used as
reference.
*More information on Map Grid of Australia can be found in Figure 5. For further information on coordinate systems:
https://docs.qgis.org/2.18/en/docs/gentle_gis_introduction/coordinate_reference_systems.html
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6. Select/activate the polygon layer in the layers panel and click the toggle editing icon from the
digitizing toolbar.
7. Add new features by using the add features tool from the digitizing toolbar.
8. As you move the mouse close to a point the point will change to show a magenta cross hairs ( ), this
means the mouse has snapped to this point. Clicking the mouse will add this point as a vertex in the
polygon. Continue following around the points to form a polygon. Right-mouse-click to finish a polygon.
9. When you finish a polygon a dialog will open to allow you to enter attributes. Click OK to add attributes
and finalise polygon.
Save your edits using the save layer edits icon on digitizing toolbar and toggle editing off
when complete.
To add, move or delete a vertex, toggle to node mode using the node tool . Click the polygon to edit.
Nodes/Vertex will appear as red squares.
Double click to add new vertex.
Single click to select existing vertex. The square will turn blue. Use the DEL key to delete
Click and drag a vertex to move.
To add a hole (donut) to a polygon use the add ring tool from the advanced digitizing toolbar and
sketch your polygon as described in step 8.
To delete a hole (donut) in a polygon use the delete ring tool from the advanced digitizing toolbar
and click in the hole.
To split a polygon use the split features tool from the advanced digitizing toolbar and sketch the
path to split. Multiple polygons will be created having the same attribution.
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Useful editing shortcut keys.
Add new feature Ctrl+. Zoom in Scroll wheel or Ctrl ++
Delete last vertex Del Zoom out Scroll wheel or Ctrl +-
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4.3 Analysing strip trial data using the moving window t-test
Following use of the Create Strip Trial Points and Extract pixel statistics for points tools, the user should
have an output dataset which contains a minimum of five columns: Columns of x and y coordinates
corresponding to locations along the trial strip and three columns of data corresponding to the extracted
pixel values from the strip ‘centre line’ and from right and left offsets to that centre line (see page 40). The
data are the input to the moving window t-test of Lawes and Bramley (2012). These data can then be analysed
in a spreadsheet or statistics package. For users of Excel, this may be done as described below. Note that in
this example, we demonstrate testing of the difference between the strip and one offset line only and use a
simple case in which no prior information (e.g. location of different management zones) is available. In
practice, users may which to compare the strip with both of the offset lines or alternative use the mean of
the two offset lines for comparison with the strip.
1. Data setup:
Column A Record number
Column B x coordinate or Easting
Column C y coordinate or Northing
Column D Data from the trial strip
Column E Data from the offset comparison line
It is assumed here that the column headings are in row 1 with the data starting in row 2.
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5 Contributors
The following individuals have contributed the production of PAT and the underpinning pyprecag Python
package, through coding, configuration and expertise in PA, and in the case of the Whole-of-block analysis
tool, the development of statistical methodology.
Core Project Team: Christina Ratcliff (lead developer), Rob Bramley (project leader) and David Gobbett
(technical lead)
Whole-of-block analysis tool: Shuvo Bakar, Warren Jin and Brent Henderson
pyprecag packaging and publishing: Andrew Spiers, Adrian D’Alessandro, David Benn and Daniel Collins
6 Acknowledgments
CSIRO’s development of PAT draws on many years of Precision Agriculture RDE across a range of cropping
sectors and variously supported by CSIRO, Wine Australia, the former Cooperative Research Centre for
Viticulture, Sugar Research Australia and the Grains Research and Development Corporation. However, the
production of the PAT toolset has been sponsored and supported by Wine Australia (Project No. CSA1603)
through funding from the Australian Federal Department of Agriculture and Water Resources as part of its
Rural R&D for Profit program (Project No. 15-02-018 - Digital Technologies for dynamic management of
disease, stress and yield). The input of Andrew Spiers, Adrian D’Alessandro and Daniel Collins was funded
through a CSIRO IMT eResearch Collaboration Project. The support of these funders is gratefully
acknowledged, as is the assistance of the project advisory panel [Dr Kathy Evans (TIA/University of
Tasmania), Colin Hinze (Bird in Hand Winery) and Hans Loder (Penley Estate)].
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7 References
Bramley RGV, Jensen TA. 2014. Sugarcane yield monitoring: A protocol for yield map interpolation and key
considerations in the collection of yield data. International Sugar Journal 116, 1–12.
doi:http://www.scopus.com/inward/record.url?eid=2-s2.0-
84916603197&partnerID=40&md5=f5f44e347b0ac4a1e0d35d95e64ddb27.
Bramley RGV, Kleinlagel B, Ouzman J. 2008. A Protocol for the Construction of Yield Maps From Data
Collected Using Commercially Available Grape Yield Monitors - Supplement No. 2. Precision
viticulture Cooperative Research Centre for Viticulture, Adelaide 1–4.
Bramley RGV, Lawes RA, Cook SE. 2013. Spatially distributed experimentation: tools for the optimization of
targeted management. Chapter 12 in: Oliver MA, Bishop TFA, Marchant BM. (Eds). Precision
Agriculture for Sustainability and Environmental Protection. Earthscan, Food and Agriculture Series.
Routledge, Abingdon, UK. pp. 205-218.
Bramley RGV, Williams S. 2001. A Protocol for the Construction of Yield Maps From Data Collected Using
Commercially Available Grape Yield Monitors. Precision viticulture Cooperative Research Centre for
Viticulture, Adelaide 1–4.
Gitelson AA. 2004. Wide Dynamic Range Vegetation Index for Remote Quantification of Biophysical
Characteristics of Vegetation. Journal of Plant Physiology 161, 165–173. doi:10.1078/0176-1617-
01176.
Gitelson AA, Viña A, Ciganda V, Rundquist DC, Arkebauer TJ. 2005. Remote estimation of canopy
chlorophyll content in crops. Geophysical Research Letters 32, L08403. doi:10.1029/2005GL022688.
Lawes RA, Bramley RGV. 2012. A Simple Method for the Analysis of On-Farm Strip Trials. Agronomy Journal
104, 371-377.
Minasny B, McBratney AB, Whelan BM. 2005. VESPER version 1.62. Aust. Cent. Precis. Agric. McMillan
Build. A 5. https://sydney.edu.au/agriculture/pal/software/vesper.shtml.
Panten K, Bramley RGV. 2011. Viticultural experimentation using whole blocks: Evaluation of three floor
management options. Australian Journal of Grape and Wine Research 17 136-146.
QGIS Development Team 2017. QGIS Geographic Information System. Open Source Geospatial Foundation
Project. https://qgis.org
R Core Team 2018. R: A language and environment for statistical computing. R Foundation for Statistical
Computing, Vienna, Austria. http://www.R-project.org/.
Gillies S and others. 2011. Fiona is OGR's neat, nimble, no-nonsense API. Toblerity.
https://github.com/Toblerity/Fiona
Gillies S and others. 2013. Rasterio: geospatial raster I/O for Python programmers. Mapbox.
https://github.com/mapbox/rasterio
Taylor JA, McBratney AB, Whelan BM. 2007. Establishing management classes for broadacre agricultural
production. Agronomy Journal 99, 1366–1376. doi:10.2134/agronj2007.0070.
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CONTACT US FOR FURTHER INFORMATION
t 1300 363 400 CSIRO Agriculture and Food
+61 3 9545 2176 Christina Ratcliff
e [email protected] t +61 8 8273 8157
w www.csiro.au e [email protected]
w https://www.csiro.au/en/Research/AF w https://people-my.csiro.au/r/c/christina-ratcliff
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